Evidence map›Paper›PMID 40777391›Full record

ArticlebioRxiv : the preprint server for biology2025

Efficient Grammar Compression via RLZ-based RePair.

Rahul Varki, Travis Gagie, Christina Boucher

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Rahul VarkiDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32607.ORCID 0009-0003-5721-9484
Travis GagieFaculty of Computer Science, Dalhousie University, Halifax, NS, Canada.ORCID 0000-0003-3689-327X
Christina BoucherDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, 32607.ORCID 0000-0001-9509-9725

Funding

Developing Computational Methods for Surveillance of Antimicrobial Resistant AgentsR01AI141810 · NIAID · UNIVERSITY OF FLORIDA · PI BOUCHER, CHRISTINA, PROSPERI, MATTIA · 2019 to 2023
$2.1M
NIAID NIH HHS R01 AI141810
6 · The paper itself

Abstract

Among grammar-based compression techniques, RePair is a notable offline encoding scheme known for its simplicity and powerful combinatorial properties, producing compact grammars by repeatedly replacing the most frequent adjacent pairs of symbols, known as bigrams. However, RePair's memory usage scales poorly with input size, as it loads the entire text into memory. In contrast, Relative Lempel-Ziv (RLZ) parsing offers a scalable and lightweight online encoding scheme that losslessly represents a text in terms of phrases that refer to a reference string, but it often fails to expose deeper structural patterns. We introduce an algorithm that produces a RePair grammar from the RLZ parse of the input, leveraging the strengths of both methods. Our method, RLZ-RePair, performs bigram replacements systematically, preserving the integrity of the RLZ phrases throughout the RePair iterations. When the reference is well chosen, our method achieves the same grammar as standard RePair while significantly reducing both memory usage and the number of bigram replacements. In particular, we show that RLZ-RePair uses significantly less memory than RePair, which required between 18% and 480% more memory across different data sets. To our knowledge, RLZ-RePair is one of the first scalable methods that constructs exact RePair grammars, resulting in a grammar-based compressor that is both practical for large datasets and faithful to the theoretical elegance of RePair.

Identifiers

PMID40777391
PMCPMC12330530

What OpenQuestion holds

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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.